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Table 1 Parameters and their values for tuning the function.

From: A knowledge-based structure-discriminating function that requires only main-chain atom coordinates

scan component parameter initial value scanned values selected value
1 DIST b 12.0 9.0, 10.0, 11.0, 12.0, 13.0, 14.0, 15.0 12.0
   c 0.627 0.525, 0.550, 0.575, 0.603, 0.631, 0.661, 0.692 0.661
2 DIST sequence separation limit 5 2, 3, 4, 5, 6, 7, 8 5
3 DABG range of the bin averaging    
   distance 1 0, 1, 2 0
   α angle 0 0, 1 1
   β angle 0 0, 1 0
   γ angle 2 0, 1, 2 1
4 DABG sequence separation limit 5 2, 3, 4, 5, 6, 7, 8 5
5 DIST, DABG sequence separation limit of evaluation 3 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 3
6 DIST 0 count penalty 8.0 0.0, 2.0, 4.0, 6.0, 8.0, 10.0, 12.0, 14.0, 16.0 8.0
7 DABG 0 count penalty 2.0 0.0, 1.0, 2.0, 3.0, 4.0, 5.0 2.0
8 SURR radius range 15.0 9.0, 12.0, 15.0, 18.0 15.0
9 SURR 0 count penalty 0.0 0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0 0.0
10 HBND 0 count penalty 2.0 0.0, 1.0, 2.0, 3.0, 4.0, 5.0, 6.0, 7.0 2.0
11 PPDA 0 count penalty 12.0 0.0, 2.0, 4.0, 6.0, 8.0, 10.0, 12.0, 14.0, 16.0 12.0
12 OMDA 0 count penalty 6.0 0.0, 2.0, 4.0, 6.0, 8.0, 10.0, 12.0, 14.0, 16.0 0.0
  1. Short descriptions of scanned parameters of the components are shown in the order of scanning during the tuning process. The b and c of scan 1 are the constants for calculating Nexp(d). Sequence separation limit of scan 2 and 4 are the lower limit of separation between ith and jth residues that was incorporated into the respective databases. The four parameters of scan 3 are the range for averaging among adjacent database bins. The sequence separation limit of evaluation of scan 5 is the lower limit of separation applied for evaluation, not for database construction. The 0 count penalties of scan 6, 7, 9, 10, 11 and 12 are the energy penalty value when no count was recorded in the bin of the compiled database. The radius range of scan 8 is the radius of the sphere for SURR component calculation. Details of the respective parameters are in Methods. The values determined by initial scanning before tuning, the list of scanned values during tuning, and the selected values with better C α RMSD are shown. Multiple parameters in a single scan indicate the scanning of all combinations among the listed values.